At this age children are closely attached to their parents and some children have significant issues separating from their parent/s. It is likely your son may be struggling with his father being away. Particularly when a new Baby is in the scene who takes most of your time and attention.
Next Steps
Try dividing some time to spend with him.
Children do understand when you explain to them the reasons and surprisingly cope well than one thinks.
Health Tips
These days Skype and video calls help.
Get him to attend a play school perhaps.