So far the best ones I've found are: Master's Fantasy Baseball League and National Baseball Fantasy Championship

For the MFBL, their highest paid league is $2665 (although I currently don't see any openings, and their payout is over 84%). Their next highest paid league is $1080 and their payout is over 83% for this one.

For NBFC, they have a nice online league that is $350 entry and 1st prize overall is 50k. Their higher stakes entry leagues involve traveling to Vegas or other big cities for live drafts, but I'm mostly interested in the online drafts.

Anyone else have any other reputable sites to add to this list that offer high stakes leagues or better payouts than the ones I've already mentioned?