If you send a whole mss, it will probably come winging back, but most query letters get read, so I think that's the way to go. I think small publishers are fine. But they might not do the bigger print runs the big publishers do and they might not get the shelf space in the stores. I'd query the big publishers and the small ones. It depends on what you are writing.
Many small publishers concentrate on one particular area of writing.
Check in Writers Market and see who's buying what, then decide who to send it to. Even the big publishers don't pay all that much to most new writers. Doesn't mean you won't make more than that, depending on the print run and the success of the book, but that's what many people start with. Only you can decide what your priority is. Meg Ref 461.