(first post for a long time lurker.. Yay)
I've been recently using Tile Studio (
http://tilestudio.sourceforge.net/ ), and while it's not specifically NES oriented, it's a very nice graphics and tilemap editor.
I've been importing the original hand drawn tile map as a bitmap, then creating a tilemap, using the tool to draw a full block (the icon with 1234). Then I use the Remove Duplicates.
Once all thats done, you can re-export the tile graphics as a bitmap, and save export the map.. Then you have a nice reduced tileset and tilemap.
It's open source and the author is working on 256 colour palettes, but it's possibly not to hard to add in support for NES attribute tables and palettes.
Juno
edit: Forgot to mention that I use Tile Molester to 'Copy From' the resulting tile graphics to make the .chr file