This should do it:
(?s)/\*[^*](?:(?!\*/).)*\(non-javadoc\)(?:(?!\*/).)*\*/
/\*[^*] matches the beginning of a C-style comment (/* */) but not a JavaDoc comment (/** */)
(?!\*/). matches any single character unless it's the beginning of a */ sequence. Searching for (?:(?!\*/).)* instead of .*? makes it impossible for a match to start in one comment and end in another.
UPDATE: In (belated) response to the comment by Jacek: yes, you'll probably want to add something to the end of the regex so you can replace it with an empty string and not leave a lot of blank lines in your code. But Jacek's solution is more complicated than it needs to be. All you need to add is \s*
The \R escape sequence matches many kinds of newline, including the Unicode Line Separator (\u2028) and Paragraph Separator (\u2029) and the DOS/network carriage-return+linefeed sequence (\r\n). But those are all whitespace characters, so \s matches them (in Eclipse, at least; according to the docs, it's equivalent to [\t\n\f\r\p{Z}]).
The \s* in Jacek's addition was only meant to match whatever horizontal whitespace (spaces or tabs) might exist before the newline, plus the indentation following it. (You have to remove it because you're not removing the indentation before the first line of the comment.) But it turns out \s* can do the whole job:
(?s)/\*[^*](?:(?!\*/).)*\(non-javadoc\)(?:(?!\*/).)*\*/\s*