We enjoyed the Blue Boat tour, but there are other choices I'm sure equally good. Don't know about the "hopper" tours -- I guess this is like the hop-on-hop-off bus -- if so, that could be a good way to see a lot of Amsterdam in a short visit. Another option, I believe, is a pass giving you unlimited tram travel for one or more days.
Jordaan is a convenient, atmospheric, relatively expensive neighborhood west of the center. We took a walk through it but stayed near Leidseplein, closer to the major museums. What you want to do depends on your own interests of course, we enjoyed the Rijksmuseum, Van Gogh Museum, Dutch Resistance Museum, Amsterdam (history) Museum, Old and New Churches, canal boat ride, flower market, Vondelpark and various squares, and walking through various neighborhoods. Didn't get to the Anne Frank House because of long lines and stairs. Skipped the coffeehouses and saw a little of the red light district on our way elsewhere. It's a beautiful city, very easy to get around.
One big downer for us was all the bike traffic, which made crossing streets much harder. They have an excellent network of bike lanes separated from the roadways (and also used by motorcycles, which at least you can hear coming). We had trouble staying out of the bike lanes while waiting to cross the major streets, because we weren't used to such an arrangement and the oncoming bikes were quiet. My wife got hit once and I'm sure we slowed down more than a few bike commuters. Don't get me wrong, the bike culture saves a lot of congestion and pollution, but the Yankee pedestrians must be careful!