According to my stats the Lv.50 one is the best, but only very slightly ahead of the Lv.80 one. This is assuming the probability for a bonus stage is the same for both (I got 4/5 on the 50 currently and 5/5 on the 80).

Assuming 90% probability for a bonus stage I average 168 trophies per stamina on the 50 stage, 166 on the 80 stage.

For the curious, here are my calculations:
Lv.15: Average 988 (only one run), 1/1 bonus rate (Lv.25)
Lv.30: Average 1392 (only one run), 1/1 bonus rate (Lv.25)
Lv.50: Average 4170 (4184, 4800, 4368, 3112, 4384), 4/5 bonus rate (Lv.50)
Lv.80: Average 4814.4 (4316, 4580, 4828, 5020, 5328), 5/5 bonus rate (Lv.80)

Lv.25 bonus: Average 1440 (1324, 1556)
Lv.50 bonus: Average 4703 (4820, 4740, 4548, forgot to note one)
Lv.80 bonus: Average 9386 (8760, 9704, 9136, 9944, forgot to note one)

That said, I first used suboptimal setups for both the 50 and 80 runs. However, the freak 3112 yield from the 50 was on the optimal setup. Not sure what that was about...

Here are the trophy/stamina calculations based on bonus stage chance:

	50%	60%	70%	80%	90%	95%
Lv.50	130	140	149	159	168	173
Lv.80	119	131	142	154	166	172