last time we were in plymouth we went to the eden project on the train. not cheap but the journey is fabulous - and a treat in itself for our 4 yr old. there's a bus link from the station so is very straighforward.
We tend to go to Bigbury for the beach, there's a decent beach cafe there as well.
Ds2 keeps asking to go to Woodlands, never been so have no idea what its like. Morwellham Quay out at Tavistock (has a mine ride and cart rides) but haven't been there for years. I'm sure it used to canoe from there....
Boat trips- plenty of 'dockyard and warships' rides from the Hoe or Barbican, or ones that go further afield. The aquarium is good. If its not too breezy swimming at the Lido or there are free open air pools right next to the sea at Mount Wise (less than salubrious area though.... the Lido is a bit less scary, and quite cheap I think although I haven't been!) You can climb to the top of Smeaton's Tower. DS1 loves that.
Sparkwell animal park (?? might be called Dartmoor wildlife park) has ust reopened. It used to be a bit dody but has been bought out and completely refurbished. Heard on the grapevine its much improved. Dartmoor's always a good place to go if you like that sort of thing.