if zed is on vilemaws lair. can he use his ability to swap places still with a shadow clone if the clone is at base?

Yes — he can activate the ability, but the swap won't fully resolve. Zed can't move from Vilemaw's Lair to base (its restriction "Units can't move from here to base" blocks that half of the move), so he stays at the Lair; the Shadow Clone still moves from base to the Lair, and both end up at the Lair together.

This matches the Tideturner/Azir swap rulings: the effect is legal to use, but instructions that can't be followed are ignored, and the rest resolve as much as possible (Rule 356.3.e.11; FAQ #8, #5932). Only a recall effect (which is not a "move") could get Zed out of the Lair to base.