Are you sure you need a sub - surf modifier ? I find using sub divide on edge rings or edge loops around the windows gives more control. You can also try sharpening or crease the inner edges of the windows . Sub - surf can create problems so I keep the mesh simple , smooth , quads as far as possible .
I’m very far from knowledgable though so listen to others - they probably know more than me .
Looks like you are nearly there - just need more edges close around the windows .
On reflection you most likely will benefit using a sub -surf mod but only once you’ve got the mesh as clear as poss.
Have you tried recalculating the normals ?
When using a Sub-surf you cannot have a ring of tris (three sided polygons) at the nose of the aircraft, you will get odd effects as you can see on your mesh. bring the quads down to a small size, then fill the end with quads only by selecting some edges opposite each other and using the F key.
All cockpit windows on jet liners are flat, so you need to mod the topology to show that. Curved, toughened glass is extremely expensive to produce compared with the flat variety, hence why they are flat.
You need to space your edge loops more evenly away from the window pillars, select the vertices and key GG and drag them down the mesh so they are spaced more evenly.
Ideally before you model such cutouts as windows, take a copy of the fuselage mesh and give it a new name. Then add a Shrink-wrap modifier to the real mesh with the copy as the target object - this keeps the mesh in shape as you cut the windows. It is also a good idea to use the I key in edit mode to make islands for you windows rather than to delete faces. The islands can also be extruded a very small distance to control the shape of the mesh around the window cutouts. You can apply the shrink-wrap to a vertex group so not all vertices are bound to the target mesh, this allows you to move them away in localised areas.
Aircraft fuselages are quite difficult to model without the creases and other anomalies. When I get back home from Australia later this week, I can post you some examples that might help.
Johnathan Williams has some great airplane modelling tutorials at https://cgcookie.com/course/introduction-to-hard-surface-modeling/ that might help you as well. You get the first one free and then it’s $12 for all the rest as I remember, this is money well spent and will save you a whole lot of time and frustration.
Next i raised the “crease-value” around the Windows AND also i modeled the interior of the cockpit (now they have windows so you can’t look inside without a glass material )