The person getting Jeter is getting the better deal, but there are a lot of factors to consider. Jeter had 30 stolen bases last year, but the two years before that he only totaled 36 combined, so Werth may out-steal him this year. Werth is also likely to hit a lot more home runs and get more RBI since he is more in the middle of the lineup.
Jeter is Mr Predictable in fantasy baseball. You can guarantee him to hit about .325, 15 HR, 105 runs, 70 RBI, and about 20 stolen bases. With Werth you can expect about .270, 33 HR, 98 runs, 98 RBI, and about 20 stolen bases, but Jayson Werth has only had one great season and he's over 30 now so he's not such a sure thing.
Another important thing to remember is position depth. There are a ton of outfielders that can produce for a fantasy team but you might cry if you don't get one of the top 7 or 8 shortstops because there are so few that can be productive. That's why Jeter might be more valuable even if Werth gets better statistics.
If the team getting Werth has another good shortstop than it's a great trade for them.