What I did was to explore the entire swamp and mark the crypts before doing anything else. Then I sailed my long ship as close to all the crypts as I could get it (some center point between the crypts that I found). Drop a work bench and a portal so I can repair the boat and then drop a few more workbenches around the area so that things don't spawn in that area when I'm walking back to the ship.

Build a work bench and a chest or 2 outside the crypt plus another portal and go in and explore and mine. When your pick breaks or you are at capacity go out side and put your scrap in the chests and portal everything else back home. Get dry and get your rested bonus back and take the portal back to the crypt. Once the crypt is clear carry the scrap to the ship and put it in the cargo hold. On your last trip dismantle the portal by the crypt and mark the crypt as cleared on your map.

Repeat until your cargo hold is full of scarp, you have emptied all the crypts in that swamp, or you are tired of grinding scrap, dismantle the portal (or leave the portal if you are going to return later and get more scrap) and sail the scrap (and portal parts if you dismantled it) back to your base.

After you unload the ship at your base, if you left the portal for later, you can chop the ship to bits at your base to recover the materials and then portal back to that swamp with the parts and rebuild the boat.