I don't know for certain. I've heard that Gemini may have been the highest capacity, but that Dueling Dragons at IOA either matches it or beats it slightly. I've personally clocked Gemini at 3,400 PPH, which is absolutely amazing. Ron Toomer himself told me that in 1979, they actually had the thing running at 4,000 PPH, but 4,000 PPH would require a dispatch interval of 54 seconds; with three sets of trains and a ride time of 2:42, that means a dwell time of 0 seconds. So I don't think 4,000 PPH is possible unless the ride time was shorter in 1979 than it is today... :)
(I have clocked Gemini ride times as fast as 2:31 and as slow as 3:04, so maybe it is possible. Oh, and the average ride time is 2:42, not 2:40 as the script says. :) )
--Dave Althoff, Jr.