Ok, I'm assuming you're talking about the high level green crafted gear, and the armor obtained using tomestones from Rowena's merchants? Ok, to start with, in general items with a higher item level are better. They will have higher defenses, vitality, and your main stat (str for most melee, dex for bard and ninja, mind for scholar and white mage, int for black mage and summoner). At most, crafted gear can go up to the second best item level out there, which is currently 110, while items from tomestones can go up to the highest item level, currently 130.

One thing that complicates matters is that you can also purchase level 110 gear with tomestones (and in fact the level 130 gear has a weekly restriction on how fast it can be earned, so you may wish to do just that). Crafted gear can simply be purchased, but the highest level crafted gear is prohibitively expensive, and some of the materials used are actually purchased using the the tomestones used to purchase equal level gear. In any case, using tomestones is definitely easier.

Now, so far it seems crafted gear is pretty poor. There is one place they shine however: Secondary stats. You can add materia to crafted gear, but cannot add it to tomestone gear. This allows you to ensure that every slot hits the cap for a stat you desire. This is commonly done for stats such as critical hit rate, or to have rings that both increase vitality AND your main stat.

So, to make a long story short, you can pretty much ignore crafted gear UNLESS you're looking to push the absolute most out of your stats, in which case crafted gear may eke out as slightly better.