Inkscape is nice vector drawing program, especially for illustrating Latex documents. In the past, I've always exported to eps first and then converted the docs to PDF using epstopdf. This way, the bounding box is confined to the actual region of interest.
Unfortunately, transparency information is lost in the process. What works, though, is to fit the page to the selection just before directly exporting to PDF. Go to File > Document Properties and press Fit page to selection on the Page tab.