Yes, you may place a custom filter on your project. In your project explorer view, there should be a white, downwards pointing arrow near the top of the panel by the Package Explorer tab. Click it, and go to Filters. From there, you can specify certain folder patterns you do not want detected by checking the box next to Name Filter Patterns. In this case, I would put the name of the 3rd party library.
Filters will hide resources from view, but they're still in the project.
If you create a project in another location you can create linked resources to the folders you want to include in your project.
The way I've always done it is to explicitly check out projects as peers. e.g:
~/myworkspace/goodproject
~/myworkspace/3rdparty
then import only "goodproject" into eclipse. If "3rdparty" is a subdirectory of goodproject, you can fake it out... Say for example your svn project looks like this:
project/
src/
main/
3rdparty/
You can locally create project/src/ then checkout only the "main" directory, and have eclipse rely on a packaged version (e.g. point to the jar if your project is java).