Absolutely, during that time you could legitimately say the top 4 EPL teams were the 4 best teams in Europe. Barcelona were on the way down after they lost motivation following their 2006 victory, Madrid were poor in Europe for a few seasons before that and even after (really not until Ronaldo and Jose came into the team did they become a force once again). The Italian teams were also declining, Juve had been relegated, Inter took up their best players but still had a relatively weak defense, AC Milan's players were aging though they managed to win one more title (had they faced a full strength United, it might have been different). The Bundesliga as a whole was not at the level of the rest of the leagues, they suffered a bad decline in the early 00's and only started recovering in the latter half of the decade (though still no where near the EPL).
The EPL (post 92) never was before and has been since as strong as it was then. You can argue it's more competitve today with more teams having a realistic change of being in the top 4, rather than it being the same from 2005-2009, but that is only because the quality of teams at the top, in particular United, Arsenal and Chelsea, has declined since then. Even Liverpool decline from their days under Rafa until Klopp came in.
During those days, the only team able to knock out an EPL team in the UCL was a fellow EPL team, no other team in Europe stood a chance. From the 2006 to 2009 I can remember Liverpool beating Barca and demolishing Madrid, Arsenal easing past AC Milan and United beating Inter and Barca.
