You may not be able to access seat selection online with a booking not made directly with Aer Lingus, but calling them might work. Seat assignment on transatlantic flights (as you are discussing business class I assume you are traveling long haul) is free, apart from exit rows. Paid for seating refers to short haul routes within Europe.

Can't help with GC points but they sometimes offer quite reasonable paid upgrades to business class. I don't know if it's possible with travel agency tickets but if you call about the seats it might be worth enquiring about pricing.