I've tried looking for websites on the consolidation to link to, but they all seem to be written by a certain type of romantic Brooklynite who is still bitter about the loss of the independent city of Brooklyn. They are not very useful.
It should be noted that the only borough-to-be at the time that had a major heartache over the formation of Greater New York was Brooklyn, or since, except for an attempt by Staten Islanders to secede during a short period when the city had an African-American Mayor.
Anyway, here are some facts that may be relevant, from the associated Wikipedia article:
* Greater New York was first seriously proposed in the state legislature in 1857, so the proposal went through four decades of debate.
* In the USA, state legislatures are sovereign over lower level bodies and can arrange local government pretty much as they see fit, though the courts have imposed some limitations to this mainly invoking the 14th Amendment and in fact eventually did override aspects of the New York State government's plans for Greater New York. So there was no requirement to consult the voters in Brooklyn or elsewhere (and I don't get the impression there were any referenda elsewhere) at all.
* The consolidation seems to have been done in conjunction with something of a power-grab by the state legislature, New York City has comparatively less home rule or power vs. the state government than is standard for other large cities in the US.
* New York (Manhattan) annexed the portion of the what was to become the Bronx west of the Bronx River in 1874. At the time, the area that became The Bronx was part of Westchester County.
* The City of Brooklyn itself had an aggressive annexation program, bringing the rest of Kings County within its borders.
* Brooklyn and Manhattan consolidated their fire departments in 1865, so absent the consolidation, a merger of Brooklyn and New York would always be a topic of discussion.
* Queens County was divided into Queens and Nassau Counties in 1899, with the portion that became Nassau County being the portion outside the borders of Greater New York. Their doesn't seem to have been any intention of including this area within the city.
* Westchester County was divided into Westchester and Bronx Counties in 1914, with the portion that became Bronx County being the portion inside the borders of Greater New York.
* Essentially, in 1898, the new consolidated city spilled over into Westchester and Queens counties, portions of which remained outside the city, so afterwards these counties were subdivided so that separate counties would be inside and outside the city.
* New York City is the only municipality that I know of in the United States where counties exist within the city borders, as opposed to the other way around which is the usual practice, though I think there are some municipalities that straddle county borders.
* The borough of Brooklyn is actually the most populous borough in New York City and has been for some time. The population of Manhattan reached a peak of something like 2.5 million but became greatly reduced by what amounted to the clearance of the Lower East Side/ Five Points slums, most of whose inhabitants and their descendants wound up in the suburbs.
Anyway, though I think alternative arrangements are certainly possible given the above, the Greater New York idea made a good deal of sense. If anything, the new city should have included all of Queens and Westchester counties, however the legislators in 1898 could not possibly have seen the extent of suburbanization that transpired. And of course nothing could be done, given the US Constitution, about the portion of the metropolitan area that was in another state!
Given that New York/ Manhattan had already expanded into Westchester in 1874, unless you have a POD before that, you should see further annexations by the City of New York, with Long Island City being the likeliest possibility. Also, I would expect that Brooklyn would annex some towns in Queens, such as Jamaica.
The two likeliest alternatives are no consolidation, but further annexations piecemeal by New York City and also Brooklyn, or a "consolidation lite" that creates IOTL Greater New York, but excluding Kings and Richmond Counties (Brooklyn and Staten Island), or a third possibility of a dual consolidation where Brooklyn, Staten Island, and Jamaica are also consolidated into a separate city. Any of these would lead to a twin cities of New York and Brooklyn scenario, with a good possibility that they merge sometime later. I actually think there is more possibility for variance with division of Queens and Westchester counties. Staten Island seems to have been an afterthought and maybe could have been left out altogether.