Do you have the TRD package with the upgraded battery? I think its a pretty good battery for OEM, and mine has held up well so far under the load of a number of accessories, including the winch. But I've been having the same thoughts as you, although they have been somewhat postponed after I installed the 2nd battery. Have you noticed any reduction in starting performance? Do you cycle it frequently, or run your winch fairly often?
It's a tough call - a good OEM battery can last 5-6 years (or more?) like our old Subaru. Or in my wife's case, the battery in her car died completely at 3 years. The battery can be the single most important piece of equipment in your rig, so having something you trust is good for piece of mind....