There doesn't seem to be a feasible way to ring the bell on the bottom of Beedle's airship.
It seems it might be possible to stab a pumpkin and throw it at the bell or lift up a pot and throw it.
The main problem is aiming, it does not seem obvious how the player is supposed to aim.
Best Answer
It's much easier if you use an item with aiming capabilities, like the Slingshot or the Beetle. It's possible to see Beedle before you've picked these up, however, so just come back when you get one. However, if you really want to access the shop, throwing pumpkins or pots seems like it should work (judging from the fact they can trigger switches etc. like shots), but it'll probably be difficult and time consuming.