Boston is certainly more affordable but I am not clear on how their reputations and quality of their programs compare. Is JHU's business school actually held in any decent kind of regard?

Are you comparing their online MBAs? What are your goals?

Johns Hopkins and BU both have a very good business school. 

Standard MBAs, but I've heard people claim that Johns Hopkins' MBA is a bit of a cash grab and wanted to find out if there's any truth to this. Does it make sense to consider it for something else than healthcare? I'm particularly interested in entrepreneurship after many years at managerial positions 

Every top school loses money on its full time MBA. Its not a cash grab.  BU is also very strong for healthcare, and offers an MBA focus for it.