When crafting magic items you make a spellcraft check to see if you are successful. Does the Crafter's Fortune spell effect this check, or does it only apply to skills like Craft(Alchemy)?
The spell only applies to Craft skill checks.
According to the description of the Crafter's Fortune spell, the bonus only applies to Craft.
The target is struck by inspiration and gains a +5 luck bonus on its next Craft skill check.
Normally, magic item creation requires a Spellcraft skill check, even though you are "crafting" something. If you don't use a Craft skill (such as alchemy, weapons, armor, etc.) for making magic items, then the bonus doesn't apply.
It applies if you use the Craft skill to make magic items.
And there are very limited ways to do this. One is with the Master Craftsman feat. Here is an abridged version of the feat text:
Choose one Craft or Profession skill in which you possess at least 5 ranks. ... You can create magic items using these feats, substituting your ranks in the chosen skill for your total caster level. You must use the chosen skill for the check to create the item.
In other words, you can use Craft (alchemy) in place of the Spellcraft check when creating a wondrous item. And you would get the bonus from Crafter's Fortune on the check.
The crafter's fortune spell's description says, "The target is struck by inspiration and gains a +5 luck bonus on its next Craft skill check." The skills Craft and Spellcraft are distinct skills, and the spell's luck bonus only applies to Craft skill checks, not Spellcraft skill checks, even when that Spellcraft skill check is made to create a magic item.
However, sometimes a Craft skill can be employed instead of the skill Spellcraft—the feat Master Craftsman is one way—, and, in such cases, a caster could benefit from the bonus provided by the spell crafter's fortune when making a magic item.
The target is struck by inspiration and gains a +5 luck bonus on its next Craftskill check.
This will only be relevant for magic item creating if the specific magic item requires a Craft check of some kind to create (this is often the case with crafting magic armors for example).