Unless there is too much Jungle tiles, I find trade posting them to be best. At 2f each they will support their own worker and with University you will get 2 science from all of them + 1 later 2 gold each from trade posts. Add Rationalism and you'll then get an additional science.
This makes it the biggest tile source of science in the game and with this having been on the CD version of Vanilla, it does appear jungle cities were meant to be science city power houses.
Gold powerhouses were everywhere in Vanilla, especially on the CD.
(If there actually is too many jungle tiles for the city to be effective even after luxury resources are improved, I would turn first turn fresh water jungle tiles into farms on plains, but still would limit this)