Is a Navy "Flag Letter of Commendation" worth Army promotion points?

It is not, but what I was instructed to do by my chain of command is to ask it to be redrafted as a Certificate of Achievement. If you look at the Navy definition of an LOC and the Army definition of a COA they look equivlant to me. The Navy recieves promotion points for an LOC, so I imagine that was the Flag Officer's intent when he awarded it to you.

Would an Army GO letter of Appreciation/Commendation normally earn points?

I am not expert but I cannot imagine it is since a commendation letter is not an award int he Army either but congratulations!