Simply add the column to insert list and fixed value to select list.
INSERT INTO [Migrated].[dbo].[Cities] (Name, ZipCode, IsDeleted)
select DISTINCT a.City,a.ZipCode, 0 IsDeleted --0 means false
from [Legacy].[dbo].[Ziplist] as a
where (a.City is not null and a.ZipCode is not null);