Tough choice. I'd go with Spelling Bee, since you'd have better seats. I'd say Wicked, but it's better to see it when you have seats with a full view and can appreciate all the sets, costumes, etc.
Spelling Bee. I saw both last month on my first trip to NY. I knew what to expect with Wicked, and I loved it. But we sat way up in the rafters. For Spelling Bee we won the lottery and sat in the second row for $25. I'm sure that colored my opinion. But the theater is much smaller and a very unusual shape. Any tour of Bee is unlikely to have that type of stage. So I vote for Spelling Bee, with almost all the original cast and a much more intimate experience. Broadwaybox.com had some discount codes available in January, I don't know if they still do. Maybe try the lottery and if you don't win, then buy tickets at the box office. Maybe that's taking too big a risk?
Even though I haven't seen either show, I've heard the music to both and Spelling Bee seems like a fun show. The music reminds me of Schoolhouse Rock in a way lol, which is also a stage show by the way.