It depends a lot on which Tier 3 run you're talking about: how many graveyards, arenas, etc. there are. Generally, Stratum 6 pays more than Stratum 5, but you have to fight your way through Stratum 5 to get to Stratum 6. At Basil, you may or may not find a lucrative recipe that you can sell for 10,000 crowns profit. There's just too much variation to give a simple answer (without collecting tons of data on constantly shifting gates).

All that said, I often do Tier-3 runs, just because I'm bored of missions. I focus on Clockworks Tunnels-style levels, which often contain danger rooms, which are still fun.