Peat bog. If it landed there, thinking it was a nice flat grassy spot, it would sink. If it was deliberately sunk, they could use ground scan radar to get an idea of where the bedrock was, and pick a spot so the very top of the craft [and a dorsal hatch] was just at ground level, and then cover it with moss. A few months, never mind hundreds of years, and you'd never know it was there. It's a just moss covered hump in the middle of a bog.

Plus peat bogs tend to be in out of the way places.

Failing that, ie if being immersed in slightly acid water is likely to be a problem for the craft, then an abandoned quarry might be an idea. Depending on when 'insertion' into the time stream occurs an old roman or medieval stone quarry. You could park your vessel in one of the dug out galleries, or bury it under loose rock at the bottom without anyone thinking more than 'Huh, the side of the old stone quarry collapsed... better tell people to keep out of there.'