I have used the New York Pass twice, summer 2009 and summer 2011 when DD was in NYC for summer dance programs (hey mbf, what programs did your DD attend?). I thought it was a good deal in 2009 but wasn't as pleased this summer. A lot of the attractions were basically the same thing, offered by different companies. For example, they listed about a half-dozen different walking tours of different areas of NYC. Several of them looked like lots of fun, but it turns out that even though they SEEM to offer a bunch of options, you can only do ONE of them with the pass. ALSO... even though they offer ferry fare to the Statue of Liberty as part of their pass, if you want to go inside the Statue you have to get a ticket. Now, the ticket to the Statue is free, but you have to order it through Statue Cruises (only company allowed to dock at Liberty Island) and they charge you $12... which is the price of the ferry fare that your NYP supposedly includes, and no way to get around this (unless you don't want to see the statue, just go for the ride or to explore the island and Ellis Island). It was frustrating this time, and I am not sure we got our money's worth this summer... it's worth it to check out what the individual prices would be before buying a NYP, IMO.
Hop on/hop off buses...I wouldn't recommend this for daytime touring. EVERY on/off bus I have ever seen seems to be standing, stuck in traffic, where you breathe incredible exhaust while wasting your time sitting instead of touring. I would recommend using the subway during the day- safe and easy- and taking a NIGHT bus tour. Grey Line offers a great tour, we've taken it twice. Because it's at dusk/night, there is far less traffic and you actually move! It's fun to be on top of the bus, out in the night, up high among all the lights of NYC.
We stayed at the Hampton Inn Times Square North this summer. It's a GREAT location, just west of Times Square, just south of Central Park, right across the street from the theatre where Wicked plays, with a decent, free breakfast every day. I got it for $191 a night,
AAA rate, but had to reserve in Dec. for a July stay. I always always always check hotel reviews through trip advisor and have never been steered wrong. This was a convenient location for us so that DD could get to Lincoln Center or Radio City Music Hall for her classes, but we also enjoyed being so close to Times Square and Central Park. I recommend you get a decent street map of Manhattan and see exactly where everything is located. The easiest way to get around is by walking, but I wouldn't want to stay on 29th Street and think I could/would want to walk to Times Square every night...it's about 20 blocks... short end of the blocks, but still a hike. We also stayed at the Buckingham on W 57th and it was a great deal at the time (each room is actually 2 rooms with a kitchen, the building used to be apartments) BUT they completely redid the place last summer so I don't know what it's like now.
For something different try Food on Foot, a walking/eating tour. You have to buy your little noshes along the way, but the guy who runs it, Corey, is very knowledgable about NYC food, neighborhoods, etc., and shows you some crazy little out-of=the-way places. It was included on our NYC pass so we only had to pay for what we ate, not for the tour itself.
