Luckily, the cruise ship will dock at each of these ports (no need to worry about the tendering hassles). Sometimes there are stairs to disembark - but, if there is not an alternate egress, the staff are wonderful about getting wheelchair passengers on and off the ship with ease.
As for excursions, each of these ports are relatively easy to visit on your own. There are some steep inclines and cobblestone walks in Old San Juan, but otherwise the terrain is fairly even and most sites are wheelchair accessible. Not knowing how mobile the 2 men are, I would hesitate recommending one of the cruise ship bus tours. But you might want to consider hiring a van (taxi) at each port so the 4 of you can take your own city tour - at your pace and to suit your interests. It is often cheaper and may make your visits much more pleasurable.
I would love to provide more detail, but need more information from you. What are your interests? Are you beach people? Just want to do sightseeing? Shopping?