Destiny can be played in one of two ways, story mode which yields vanguard marks, or pvp which yields crucible marks. It's possible to use either of those currencies to buy related gear. Is there any significant different between the gear that costs crucible marks or the kind that costs vanguard marks? Is the crucible gear somehow better for pvp?
Overall there is not any significant difference between the gear from the vanguard vendor, the crucible vendor, and the faction vendors.
It's more about what kind of build you want to play and what kind of weapons you're comfortable with.
Also, many top level items come from things outside of the crucible and vanguard economies, such as rewards from raids, nightfall strikes, the Queen mission, engram drops, and purchases from Xur.
If you're still curious, the Crucible gear is slightly better for PvP - but mostly in terms of the "perks" you unlock. EG, compare the PvP hand cannon (http://www.destinygamewiki.com/wiki/Lord_High_Fixer) to the PvE one (http://www.destinygamewiki.com/wiki/The_Devil_You_Know). The have the same attack, and some slight variations on other stats, but for the most part are similar. The big differences are in their perks - IE, being able to view your radar while ADS (Third Eye) is more useful in PvP, whereas something like bonus damage after a kill (Crowd Control) will proc more in a PvE setting.
Items bought from either vendor can be used in either PvP or PvE. There are no restrictions on crucible items being used in PvE. The only diffrence is where the marks and reputation comes from to purchase the items.