The other issue with booking a hotel that's listed as being in Times Square is that it may actually be closer to the Port Authority. A few years back, I got one via Priceline I think. It was a fine hotel but involved walking by three porn shops and a needle bin to get to the hotel. Porn shop. Liquor store. Porn shop. Chinese food place. Needle bin. I think the probation office was on the way too. It was like a joke---I screwed up the Priceline bid. and got us that location. Times Square seemed fine I was a noob.
I did Brooklyn last time and loved it. Previously, had been on the Upper East Side, near Grand Central, Central Park South, over by the UN, Wall Street., Chinatown... I've bounced around and really enjoyed most of the places I've stayed. The subway is everywhere. I've yet to stay anywhere that's more than 3 blocks to a subway stop. Some places have the stop closer to the hotel entrance, but I've never felt stranded anywhere.
Near your hotel, more than any tourist site, you want a sane place to get breakfast and coffee, one that won't be beyond mobbed when you try to go. I prefer a neighborhood rather than a touristy feel Lines move more quickly. You don't have tourists in front of you taking forever to order, etc. You want to be close to a decent place to get breakfast on a street that has the usual drugstore, ATM etc. Once you're up and about, you'll be all over the city. That's my two cents.
Edited: 12:10 am, January 12, 2014