Open a terminal, go to the directory with all these files: cd complete/path/to/directory. On a Macintosh, complete/path/to/directory can be obtained by dragging the relevant folder onto the terminal window from the Finder.
Translate them all: apply epstopdf *.eps (yes, the apply command iterates over all files).
If your files are located in subdirectories, the find command may be of use:
find root/directory -type f -name "*.eps" -exec pstopdf {} \;
Replace root/directory with the name of the top-level folder the search should start.