tree viewers have been discussed around here a few times before, so you can even try browsing BioStar for such information. my personal option, and I should say that I'm not a phylogenetic-centered bioinformatician, would be Archaeopteryx (what a name!), the successor to ATV based on the forester libraries. it is the sugested interface for the phyloxml syntax, which I have found great to represent any tree I have had to deal with.

Have a look at Epos, it is a Java library and application that can do a lot of weird things with phylogenies, multiple alignments and trees. Among other things it can display a tree with inner node labels. The search function allows to search for all node names and matching subtrees can be highlighted. If it can handle a large tree like yours could be worth a try.

See this What phylogeny viewing software do you use? . It asks a similar question and/or the links provided therein could allow you to do what you need. I would also look at the links provided in Roderic Page's blog, iPhylo. Phyloviewer and Topiary Explorer are two viewers that you should check.