Hi Sarah -
As a Yorkshireman I'm probably contractually bound to say, yes, get on that York train and head for either the Dales or the North Yorkshire Moors.
That said, if you wanted to go somewhere different this time, you could get a train to Windermere as easily from Manchester (more connections involved) and enjoy the delights of the Lake District. It may be pointed out that the Lakes get thoroughly booked up in summer and this is true, but as an alternative you could base yourself at the head of the Kent estuary in Arnside which also has a rail connection, although getting to the Lake District proper from there might be a tad problematical - some research into public transport connections would be sensible - our friends have had a 'pied a terre' at Arnside for years so generally when we visit we have a car.
If you don't mind driving you could probably hire a car in the vicinity. There's plenty to do in the area, lots of great pubs - the Albion in Arnside to name one - excellent coastal and fell walking - Arnside Knott or train to Grange over Sands and walk to Cartmel and back by way of Hampsthwaite Fell, or if they are happening, join a walk across the quicksands of Morecambe Bay (zip offs or shorts and sandals and change of footwear for this, you get wet as you have to wade the channels!) from Arnside to Grange with the Keeper of the Queens Sands, info from Tourist Offices, but don't try do the latter by yourself, it's dangerous!
If you can get accommodation in the Lakes (I'd suggest the Coniston/Eltermere/Langdale area for plenty of what you are after and as personal favourites, forget Keswick it will be rammed!) then in my opinion there's nowhere finer in England!
Hope I've given you some food for thought, but whatever you choose, have a great trip!
Ian