Whereabouts in Manchester are you? do you have transport.
Things I have done with my 4.11 yo are:
Swimming - good for rainy days. The Aquatic Centre has family time every morning 10-12.
Lyme park - has activity for children on certain days. I went on a Wednesday.
The 'Miffy' exhibition at Manchester Art Gallery is good for a few hours followed by lunch on tampopo.
The science and industry museum (has a train ride).
Stockport Hat museum has workshops for 4-11 yo. My dd went to the kite making one and loved it.
Other parks: Bramhall park, Tatton park, Bruntwood park all have good play areas for children.
Reddish Vale country park has a small farm.
I'll give it some more thought and post again. In the meantime others' suggestions would be useful to me too!