A series three cell LiFePO4 pack is only going to produce a nominal 9.6V, NOT 12V. If you have a three cell pack that produces ‘12V’, those cells are either LiCo or LiMn. Of course, the voltage characteristics of a three cell LiMn/LiCo are going to be MUCH different from a four cell LiFePO4 pack. For 12V, LiFePO4 is MUCH, MUCH, MUCH better than LiCo or LiMn, particularly as a lead acid replacement.
As far as the largest capacity 18650 LiFePO4 battery, Fasttech sells an ‘1800 mAH’ protected (WHY!!!) cell and a ‘2200mAH’ cell. Keep in mind that these numbers are substantially higher than most any other cell I have seen, so I consider these numbers to be suspect. Like the other guy, I would consider anything much over 1500mAH to probably be unrealistic.
On the other hand, unlike LiCo, going from an 18650 to a 26650 gets you MUCH more capacity. Expect to get anything from around 2500mAH from a high current cell (like the A123 Systems 26650 ) to 3300mAH from a lower current cell. So if you CAN go with a 26650, this would be a better choice if you NEED more capacity.
For even more capacity, consider the 5000mAH Feilong 32650 . Tests have shown this to be an AWESOME battery. The voltage of that battery makes NiMH look downright unstable!