I believe he was with the Marines. Possibly in some kind of special ops capacity. As such, he would have operated with all sorts of other units, including swiftboats.
I served in the 164th CAG (Army) out of Can Tho which spported the entire Mekong region with insertion and retrieval, recon, air support, resupply, medavac, etc. We worked closely with the Swift Boats on many occasions. Having Marines on the boats for any shore activities was standard practice. This further undermines Kerry's story of going ashore to dispatch the wounded VC. (Only Captain Kirk left the bridge for such missions)