We took our first trip to NYC in 2008 and we used Grayline tours as our primary transportation. I loved the Grayline tours. Our tour guides were very knowledgable about the city and we were impressed with their dedication to their job(except one old witch!) Be aware that they do ask for tips from time to time. The first time we experienced this we felt uncomfortable, but the longer we stayed on the tour the stronger we felt that these people really *worked hard* for their tips and we were glad to give them a few extra dollars.
We move slow, so we choose the 72 hour package. That way we didn't feel forced into racing from one thing to the other just to get our money's worth. Taking the Grayline buses helped us get the lay of the land. You ride awhile, then get off and see stuff. then you can get back on and go ride awhile more, then go see stuff.
We had the package that included tickets to the Statue of Liberty and Ellis Island. One word of warning: either make reservations for the ferry or get there very early, by 8am, if you don't want to stand in a mile-long slow-moving line. We got ourselves to Battery Park by 8:30 and were some of the first on the ferry. There's not much to do at the Statue of Liberty, so we didn't get off there. It was really neat to circle the monument. By staying on-board we were among the first to Ellis Island, which I HIGHLY recommend. We had family members who came over from Greece and Wales, so it was a really emotional experience for us. We spent 6 hours at Ellis Island.
Good luck with your trip. I'm sure you could see the same things without the Tour, but for us it was a necessity. DH is disabled so walkign long distances is out of the question. For us, the Tour fit the bill