I think you mean Ancient Thera, in which case it is about an hours walk up the hill from the centre of Perissa. It is closed on mondays.
Akrotiri is still closed, I believe.

We have actually walked from Perissa to Akrotiri, a few years back. I can't remember exactly but think it took a couple of hours (?), we then got the bus back. The walk was mainly on the flat, unlike the short but steep walk to anciant Thira. I think Ouzo is right though and Akrotiri is unfortunately still closed, after the protective roof collapsed some time ago.