All Pokemon cards have strengths and weaknesses, but in terms of raw power, the two Mega Charizard EXs from the Flashfire expansion are the strongest. Their attacks both do 300 base damage which is the highest in the game, as of 2014.
To give a perspective, currently the Pokemon card with the highest HP is Wailord-EX at 250 HP. The Mega Charizard-EXs are strong enough to one shot everything in the game right now.
There are a few Pokemon cards that have attacks that can do extra damage if certain conditions are met. In theory, some of these cards have the highest damage potential, although the conditions for pulling off the maximum amount of damage are not easy to accomplish.
It is likely that there will be stronger cards in the future because trading card companies create stronger cards to drive sells.