When we stayed in West Manhattan in June, we did the Top of the Rock as my DD wanted to go there rather then the Empire. So we did, and luckily, the military discount the Rock gave was much better than the discount the Empire was offering. Only info I got from a local we met, was don't bother to go up, unless a clear day. We were lucky too, as that morning it was lovely out. We did buy our tickets when we got there. Though the elevator was crowded, there was enough room in the floors you could look out from, that you could take pictures with no one else around you. Views were great, and took about an hour or so, from the time we first entered the building. I sat on a bench up there, for some time, as it was so nice out. But with anything, summer crowds can be there. We were there the 3rd week in June, a Wednesday, Thursday and Friday. We did the Rock early on that Thursday.
Central Park is huge, and we entered from the one near 70's? street. We walked as far as the Balto statue, and just walked past the little Central Park Zoo. Nice pathway, and some parts shaded, that helped. Times Square was always busy, but we enjoyed seeing all those screens and neon. We toured in daylight, and spent some time at night there.
We only spent 2 nights, as just a quick trip, as I had got a last minute absolutely awesome seat location for the 9,000 show of Lion King, on Broadway, the first night we stayed there. Over those 3 days, we waked almost 60 miles. My feet were very tired by the end of each day. We just did not have time to see Ellis Island, though if we had time, we were going to take the free ferry ride. We didn't get to the Brooklyn Bridge either, but have pictures of it from the Rock.
And remember, traffic is crazy, so give time to get to all the places you mention. And if you walk, make sure you have very good walking shoes. Even with my broken in running sneakers, my feet still were tired from all that sidewalk walking. And everyone walks fast. Which is why my DD said, she could so see herself working in that part of NYC. Me, eh, the suburbs are where I rather be, and am.
Have fun, there is so much to do in NYC.