First of all, you have to do:

newIndex, indexer = a.reindex(b)

reindex returns two things. You need/want to get only the indexer.

So now you can get what you want:

indexerWithNan = np.where(indexer == -1, np.nan, indexer)

Why was your initial code wrong? The reindex() method does not support the fill_value parameter for pandas.Index objects as it does for pandas.Series or pandas.DataFrame.