We are ending our European trip in Amsterdam/Brussels. We will have about 4 days on the back end and hope to travel to Brussels after touring Amsterdam. Please let me know what sights you would recommend in both cities? I understand traveling by train would be the most desirable, please confirm.
How about taking a train from Amsterdam to Brugges instead that requires a transfer in Brussels.
What are your interests? What are your likes and dislikes? When exactly are you visiting? Did you check out the websites of the tourist information of both cities to learn what you can see and do there?
Are you flying home from BRU? What month of which year? Are you prepared to buy timed, non-refundable tickets to some attractions? Which cities do you plan to sleep in?
Train would be the most obvious choice, not sure what other modes you were considering, but flying really offers no advantage, renting a car would be silly, however I suppose bus would be an option.
For trains, you can either do the fast Thalys train, or the standard slower trains. The difference in time is not that huge, and a standard train would allow a stop in Antwerp if that has interests.
You could create a long list of things to see in Amsterdam, for Brussels, it is mostly the Grand Place and surrounding area that draws, there are a number of museums, not big world status places like the Rijksmuseum and Van Gogh in Amsterdam, but great museums if their special interests match yours. The city itself is touristy, and very gritty/urban. To be honest, unless your interest is beer or something specific, it is worth a day, but little more. I enjoy Antwerp and Ghent more.