Was it less than Manning's deal? Yes; Manning got $14m/year while Brady got $10m/year.Even Tom's front loaded deal before was well below market value...well below.
So if you're using Manning as a benchmark, then yes it was well below market value.
However at the time the cap was $85 million. Brady was making about 12% of the cap. Is that percentage really well below market value?
Players are offered contracts in direct correlation to the cap; that's why newer contracts are so much higher than older ones - the cap has increased by 50% from the time Brady started his last contract to last year's cap figure.
Does Brady deserve a new contract that will far exceed his last contract? Yes, of course.
Is it reasonable for the Patriots to want to know what the cap is before committing to a large contract? I don't see why not. Same hold true for the Colts with Manning, Steelers with Woodley, etc.