I am not saying it would be easy, or even possible, only that the Russians knew that the Neva and Düna/Daugava/Dvina river gives access to the Russian heartland and had positioned their forces accordingly, to be able to counter any move up either river - which should be taken into account in any Sweden joins the Crimean War scenario - Russia had some serious forces along the Baltic Sea coast and a much better ability to support and reinforce them compared to Sevastopol - the rivers work both way.
I repeat, invading Russia by the riverboats is impractical idea but St. Petersburg and Riga (and other cities on the coast) had been important enough on their own to provide for their adequate protection even if Sweden was not a factor.