If the pegs are through bored holes you can get a piece of steel that is smaller in diameter and sometimes pound the peg out from the back side using this piece of round steel stock as a "peg pusher."
If the timbers are blind pegged then you'll have to pull them from the side where they were driven in.
This can be done by using a screw, such as a timberlock screw.
Bore a small hole into the peg center. Insert the timberlock screw and leave the head out about 1" or so. Use a crow bar or pinch bar and place the forked end under the head of this screw and pull the peg out, blocking up the bar as needed to pull the peg out.
If the peg splits due to old age, the put a hose clamp round the peg to hold it together while pulling.