Firstly I love both players.
Eto'o was the better player for us and more influential which is not really a surprise considering the fact that he played for us for 5 years and enjoyed his best footballing years while playing for us. Henry on the other hand arrived as a 29 year old who had suffered from a lot of injuries that sadly continued during his FCB time.
Nevertheless he was extremely influential in our treble season and will also be remembered for playing for the most successful club team that ever was (sextuple)
And Henry was not bad in his first season. Actually he was our topscorer in that season. Yeah, it was an absolutely horrible season but if Henry was uselss then everyone else was even more useless.
In terms of overall quality Henry was the better player. There was a time were he was absolutely unplayable for Arsenal.
And let's not forget that he won a WC and Euro and played a role in both (more during the Euro's)
But both were fantastic and the best strikers in the past decade IMO.