We have stayed at several hotels around Times Square, including the Marquis about 5 times. It is a great location for being right in the heart of things & the view is awesome if you get a good one.
We also really liked the Millenium, which we found on travelzoo last year. It was really close to the huge Toys R Us! And I remember the deal being really good for NYC.
Our fav is the Royalton, which we have also found on travelzoo. It is more of a trendy boutique kind of hotel though.
LOVE travelzoo for those kinds of deals! And priceline has worked as well (can't remember now, but I think we got the Marquis once).
We are looking to go again soon (with the kids this time, they have never been). We live pretty close, so we try to go a few times a year.
Good luck!