There is no connection by the river between Prague and Budapest so you will probably go from Prague by bus toward the Danube or its navigable tributary. What would be more economical? That changes case by case. If you can fly directly into Prague, do it. But as I am aware there are only two direct flights from the US into Prague. One from New York and one from Atlanta. You should have at least three full days for each Prague and Budapest and even then you are only touching surface. Prague is famous for its crowds. The medieval center streets are very narrow. The worst is so called Golden King Way. Start early and you will share Old Town, Charles Bridge, Little Quarter and Hradcany Castle with just few people. After 10 am forget it and do some other parts of Prague also in the center like New Town, Vysehrad, Petrin, etc.