There is technically no difference. This question comes up from time to time, as there are a lot of variations.
In Japanese, 瓶 is the character for 'bottle' and is 99% of the time pronounced "bin." I just double-checked an online dictionary and of the 44 entries that have the 瓶 character, the word "houbin" is the only one that also says "houhin." But there is evidence that 'hin' may be an old pronunciation that has stuck.
Even in Japanese, we'll see vendors list the item as 泡瓶 or 宝瓶. Both of the first characters are "hou." I think the first one (泡: bubble, foam) was more original, but the second one (宝) means "treasure," so that one may have crept into use.
If you're really curious (and still with no solid answer), I asked this question on a Japanese language forum awhile back, and you can see our discussion over here
; the first few posts cover the main part, the rest is a discussion on a spammer comment.