A crate is probably best, particularly with a pup. I have used the harnesses that attach to seat belts, and with my most recent boy I used one of those "hammocks" that attach to the headrests. He had a crate phobia, but was happy in his hammock. As far as protection in a crash, I don't think anything is foolproof, and the aftermath of the accident will vary. You don't want a loose dog on the highway, but you don't want one trapped in a crate if the car goes into water or there is a fire. Not possible to guard against all eventualities, but for most a crate is likely best.
Traveling alone, I would go with the seatbelt harness thing. It gives your dog freedom to move around, but keeps him from hopping from seat to seat. My dog gets carsick, so we never take him anywhere without someone else to catch his throw up (he knows to barf in the barf bucket). He can last about a half hour on his medicine and then he gets antsy