Novosibirsk is the third largest city in Russia, so that might work.
Are we really talking about pre-1900 PODs? Because before Novosibirsk was founded in 1903 (before that there was a village with less than 1000 people). The whole population of Siberia in 1897 was just over 5 million people (comparing to the 130 million total population of the Empire). To be fair in the Asian part of the Empire did also include 7 million people in Central Asia but it was effectively a colony and even if we count it the population of European Russian Empire was 10 times bigger than the population of Asian Russian Empire.
It seems like people look at the map of Russian Empire and believe that it has evenly distributed population/industry/whatever. Even
today Russian mean center of population is near Izhevsk several hundred kilometers west of Urals. In 1897 it was near modern Michurinsk 300 km south and 150 km east of Moscow and of course urban population, industry, educational centers etc were shifted to West by way larger margin.
Here are populations of top 10 cities of Russian Empire in 1897:
St Petersburg: 1 264 900
Moscow: 1 038 600
Warsaw: 683 700
Odessa: 403 800
Lodz: 314 000
Riga: 282 900
Kiev: 247 400
Kharkov: 174 000
Tbilisi: 160 600
Vilnius: 159 600
To answer the OP question I honestly believe that with PoD after Peter 1750 there is almost no chance of Russia having capital in any city other than Moscow and St Petersburg.
There are two main reasons for relocating capitals. It can either be a result of compromise between different regional groups while organizing a country or ruler/government trying to sever the established political links.
Once St Petersburg is an established capital Moscow is ideal for both purposes. It dwarfs any other potential candidate in Russia proper by population, wealth, educational institutions, industry, ideological and historical significance. It is also by far the most important road network nexus in Russian Empire (by XVIII century most important roads in Russian Empire go through Moscow) and even is really close to mean center of population of XVIII-XIX century Russian Empire (which would be several hundred kilometers to the North of 1897 mean center of population). Moscow is also is perfectly secure militarily (and if it becomes threatened it means that Russia is in very deep trouble because large part of its industry and population are already in enemy’s hands).
There were simply no comparably important cities in Russian Empire by any relevant metrics (Nizhny Novgorod mentioned upthread was commercial capital of Russia but only if we discount Moscow where a very large proportion of wealthy merchants resided). And creating from scratch (or almost from scratch) a new urban center capable of hosting Russian Empire bureaucracy, important nobles, guards and all the people who make their life comfortable, costs prohibitively much.
Even Bolsheviks who wanted to break with tradition as much as a next guy had no real choice but to move the capital to Moscow.
So in my opinion there are two main possibilities for OP premise:
1. Peter the Great moves capital to other city than St Petersburg. Since PoD is after 1700 Peter the Great is already fixed on Baltics (and anyway “Southern St Petersburg” makes little sense with Ottomans not allowing Russian merchants even to trade in Black Sea not to mention passing The Straits).
Other than cosmetic changes (like ATL St Petersburg being where Shlisselburg is or on Southern bank of Ladoga) the only real alternative is capital being moved to one of 3 main Livonian ports – Narva, Revel or Riga.
Each of them has its own advantage. Narva is the most secure and closest to Russia proper, but has the worst harbor, Revel has the best harbor (and has Rogervik/Paldiski harbor in 50 kms that doesn’t freeze in winter) but has the worst connection with Russia and Riga is the most important city of the 3 and is located in the mouth of Western Dvina that potentially allows the most convenient communication to Russia proper (which is actually not worth communication via Neva and Ladoga to St Petersburg) but which is controlled by Polish-Lithuanian Commonwealth.
I would say that Narva can be made capital if Peter the Great does not suffer humiliating defeat there in 1700 and Riga if Peter the Great somehow able to annex parts of PLC during Great Northern War(which is not impossible, but tricky)
2. Peter the Great doesn’t move capital, or he does, but this decision is silently ignored by his descendents (this actually almost happened IOTL – after his death the court moved back to Moscow and returned to St Petersburg during Anna Ioannovna reign)
Anyway capital effectively stays in Moscow. If at some point later a new regime is established (either by revolution or by radical reformer like Peter the Great) moving capital to other city can actually be considered. And without St Peterburg being capital there simply doesn't exist another city than Moscow such that is already has urban infrastructure ready to accomodate capital. In this case picking any town in reasonable location or even creating a new town is possible.
What this reasonable location would be depends greatly on circumstances and time when the movement happens (most importantly the situation becomes much more flexible in mid XIX century with railroads and telegraph)
All in all I would say this is a tough one and the restricting PoD by as being after 1700 makes it really challenging task.
Pre Peter the Great PoD makes finding alternative capitals for Russia much easier: if at any point Russia manages to grab large portions of PLC moving capital to any reasonable city to the west (Kiev, Polotsk or Smolensk could be reasonable variants ) can be managed. I’ll name a few possible earlier PoDs with Russia annexing large parts of the Grand Duchy of Lithuania (in which case moving capital to the west would help integrating these territories easier both logistically and politically)
Say Alexey Mikhilovich is more politically astute/military competent and instead of signing Truce of Vilna keeps pushing. Or Ivan the Terrible wins Livonian War. Or Ivan the Terrible avoids Livonian War and becomes elected/ his son becomes elected the King of Poland (IOTL he was actually a quite popular candidate despite fighting a war against Lithuania). Or even Peter the Great himself decides to attack PLC instead of Sweden.
But all these PoDs are pre 1700 and thus are disqualified by OP