The Harvest Base was the mainland site that the InGen Harvest Operation originated from on their journey to Isla Sorna. After the airlift had deployed their cargo and team on the island they returned to it to await further orders and pick up the team from Isla Sorna.
However, due to the interference of Nick Van Owen and Sarah Harding the order was never sent in the manor that was intended. The operation, which had suffered major casualties, was eventually evacuated from the island with two tyrannosaurs in tow after Nick Van Owen was able to radio for help from the Communications Center in the Worker Village.
Though not explicitly stated in the film, it is likely that the base was located somewhere in Costa Rica.