3 hours of it involves the drive to and from the tour location, which can be interesting because you see the countryside (and the poverty) but it is still a third of the tour time. The 90 minute drive back to the ship will likely seem endless, so just be prepared.
I think the longest tour we took in Central America was 5 hours and was to a pineapple plantation. It was fun and I don't regret it.
For Panama, Guatemala, Costa Rica, and other nearby ports (Colombia for instance) I do strongly urge using a ship's tour so you've got that base covered.