I think you're only going to see domestic lie flats to/from JFK and ATL on the east coast. I think DL runs lie-flat 767's LAX-ATL, so you'd still be looking at two connecting flights sitting. If SFO-JFK is offered with a lie-flat, doing that then driving may very well be your best bet.

The other option is to fly SFO-BOS on VX. Their F seats don't lay flat, but they look like this: http://www.virginamerica.com/travel/cabins.html

I've never flown them, but I hear they're comfortable.

You do have a couple of other options if time in the air and/or cost aren't an issue. You can fly BA SFO-LHR-BOS in business Or maybe EI SFO-DUB-BOS.