Yes (unless you're actually flat-footed)
The Wall of Blades maneuver itself only has one restriction on its use:
You can't use this maneuver if you are denied your Dexterity bonus to AC against your attacker.
Your Warblade (ToB, p. 20) has Uncanny Dodge, which says:
You retain your Dexterity bonus to AC (if any) even if you are caught flat-footed or struck by an invisible attacker.
So you're not denied your Dexterity bonus to AC in this case, and therefore not prevented from using Wall of Blades.
The other reason you might be unable to use the counter would be if you are unable to take an immediate action. From the SRD:
You also cannot use an immediate action if you are flat-footed.
This would be the case if you have not yet acted in this combat. So, if an invisible attacker successfully sneaks up on you and attacks, getting a surprise round in which to do so, you would be unable to use Wall of Blades to defend yourself. However, from your question it sounds like you're asking about an ongoing fight against an invisible opponent of whom you are already aware. In this case, you would be able to use the maneuver.