I've taken my kids to both Le Parker Meridien (in the past year) and the Millenium Hilton (2-3 years ago) when my parents were in town visiting, and we had a very nice time at both. Neither was terribly crowded when we were there and neither had any serious lap swimmers for the kids to bother when we were there.

Le Parker Meridien (a Starwood-affiliated hotel) is a better location for most tourists and the pool has very cool panoramic views (it's on the top floor). My recollection (hard to compare as I visited them a couple years apart) is that the Hilton pool was bigger, though. The Hilton (note this is the Millenium Hilton with one "n" downtown--not related to the two "n" Millennium hotel chain) tends to have lower room rates and I think the average room size is a little bigger, too. The pool is on a low floor so it doesn't have panoramic views, but it's in a nice room with tons of windows that still has lovely views of the historic church next door.

I once saw the Crowne Plaza Times Square pool when checking out the NY Sports Club several years ago. Because it's part of a health club, I think it's usually set up for lap swimming more than splashing around, but I think they allow kids (you might call the hotel to confirm). I don't think it has horizontal views, although from Google Images it looks like it has a glass ceiling.

The One UN hotel (a two "n" Millennium hotel) also has an indoor pool. I haven't seen it, but from Google Images it looks like it's in the same category of nice-ness as the Hilton and Parker.

And there's a new Fairfield Inn opening up soon at Allen and Henry Streets on the edge of Chinatown that's supposed to have a pool. I can't imagine it'll be nearly as nice as the others, though.