Who was believed to be the first
person to go aloft in a balloon in
the Civil War for reconnaisance ?

Thaddeus Lowe

Hmmm, I have a different answer
on this one. I will have to get
back to this when I can get to
the library this week.

Dwight has a different answer here.

Balloons in the American Civil War indicates that LaMountain's flight preceded Lowe's.

Both of the last two links indicate that LaMountain did make the the first observations, though his were not "official", i.e. done as part of the newly-created Balloon Corps.