This is really old, but for those who need to upgrade sites running EE2 to newer versions with Tagger, this worked for me.
Note: uninstalling Tagger and reinstalling it from the Add-on Manager does work, but it will erase all of your existing tags. To prevent this from happening, follow the steps below.
This is assuming Tagger is on version 3.2.1. Right after moving the EE3 files over and before running the update step, copy over the files for Tagger 4.0.0.
In tagger/upd.tagger.php, there is this code:
$module = $module = ee('Model')->make('Module', array(
Update these lines to the following:
$module = ee('Model')->make('Module', array(
After the EE update step, go to the Add-On Manager and click "Update to 4.0.0" next to Tagger in the list.