To stay at with a 3 and 5 year old I think Harbour Lake wins hands down- the pools are geared for the younger set, there is free miniature golf, great kids' activities, etc .he villas are very nice, even if not quite as nice as some of the others. The pools basically are an on site water park.
Lakeshore is reputed to be a much classier resort, and I am sure whatever you pick the kids will enjoy. I think you also need to consider if you are planning to use it as basically a resort to visit, or as a home base for the parks. Lakeshore is further from the parks, which may (or may not) be a factor you want to consider. So while it is the top resort in the area, what your plans are for the week may influence if it's the best for you.
In contrast Harbour Lake (and Cypress across the street) are a 10 minute drive to the Disney parking lot, a mile from Sea World, etc.- faster than taking a bus if staying on one of the Disney properties not on the monorail.
Since you've been asking a lot about traders- those 3BR MGV units have a lot of trade power, since size is a biggie in II; you can lock it off, or use the entire 3BR when trying for peak time/property trades. Since resale pricing is probably in the same ballpark, maybe others can chime in as to whether they feel a 3BR MGV/MGR unit will trade better than a NCV unit (assuming prime weeks reserved at both).
And, of course, the other factor- being from the East coast, with little kids, which do you think you'd be more likely to use?