"...there is irony in the fact that Boeing is heralding the potential offsets from the fighter jet contract at the same time as it criticizes government subsidies to Bombardier."

Defense is the major way the US government subsidizes its aerospace industry (and many others). Boeing have especially benefited from channeling defense project R+D into lucrative civilian ones (the B-17 bomber -> the Boeing Stratoliner, the B-47/B-52 bomber -> the Boeing 707 jetliner etc.) 

Risky, cutting edge aerospace industries all around the world need government subsidies to survive. Boeing objects when rival companies are directly supported by government money (Bombardier, Embraer, Airbus) but they are fine being propped up by military defence contracts.