Timber2 plays in the exact same league, albeit in the opposite conference, as the Riverhounds. It is the exact same level of soccer. The USL now has the league split up into eastern and western conferences and teams from the two conferences do not play each other to keep the travel down, but it's the same league. For instance the year before when the league was not split in half the Riverhounds played the LA Galaxy reserve team, Galaxy 2 in Los Angeles.
Anyway, this past season the Riverhouds were in the same conference as the reserve teams of the New York Red Bulls, Toronto FC and Montreal Impact. The Riverhounds actually made the playoffs, whereas Toronto's and Montreal's reserve teams did not (they finished well behind the Riverhounds in the standings). In the west, LA and Seattle's reserve teams made the playoffs, Portland, Vancouver and Salt Lake's reserve teams did not. In the six games the Riverhounds played against MLS reserve teams in league play the Riverhounds went 5-1-0. Unfortunately for them, the seventh game was in the playoffs against Red Bulls 2 and they lost in extra time.
So in point of fact, the Riverhounds are exactly the same level as Timbers 2, and this past season the Riverhounds were almost certainly better.