Hmm, being inland is where it’s at! Even with a 60m rise in sea level nothing changes in Toronto.
Perhaps, but the upside is that when I order Calimari at my local Greek establishment, I stand ( swim ) an excellent chance of it being remarkably fresh. 
friedo, we’ve begged you to leave Brooklyn. Now, you have a reason. Don’t come to Queens unless you love sleeping with the fishes. 
Back to the OP’s concept of buildings continuing on with their bases under water. Beyond structural concerns due to flooding it’s impossible for most buildings to exist in a usable way in anyway similar to what they are now.
Skyscrapers have require incredibly complex electrical and mechanical systems to remain habitable. Flooding the lower stories would reek havoc on these. Take out the plumbing or electrical in a place with 3000 people in it and no one will want to be there.
Electrical, Internet, water, sewage, HVAC. All can be provided above ground. Question is, is it cheaper to do this for thousands of buildings or to move 10 million people to higher ground?
Maybe it is time we moved NYC. 