Another option is American Express Travel. I just booked a VS-BA combo (thanks to Google Flights), and they were able to put together combos that weren't showing online anywhere. It seemed like they were able to get around what looked like "married segment" logic* on ExpertFlyer that didn't show the correct inventory on the flight pairs, and could piece together flights that individually had the correct inventory. In other words, I had a lot more flexibility in which flights I wanted vs. what I was able to get to show on the regular OTAs.
*I'm not sure I understand how one carrier can applied married segment logic to another carrier's flights, so not sure what exactly was the problem.