My timelapse is bad quality?

Recently bought the nikon d5100, made a few time lapses [using the in camera intervalometer not an externam one] when I upload the photos, they are roughly 4000 by 3000 pixels, yet when I make the timelapse using sony vegas pro, the video is terrible quality, help much appreciated.

What are the settings within the software, does it reduce the size? (resize/resample)

Bad quality is very vague, could of be a number of different problems and bad in a many ways, and it will be hard to tell without at the very best a better description. I think it's best if you post a sample of both the timelapse and a few of the original images.

The resolution created by Sony Vegas (or any other movie editor) will not be 4000 X 3000 pixels, even HD is only around 1024 X 768 or 1600 X 1200, the program may be defaulting to a base level 800 X 600 or even 640 X 360 pixel resolution. Sony Vegas is reducing to these resolutions on the fly (worst possible option) it's much better to reduce them first in an image editing program, then you can see what each image will look like.

You need to set the resolution and aspect ratio you want the final movie to be in the setup part of Sony Vegas. You set this for the device the movie is going to be played on which will be usually much lower than you think.

You are slowing yourself down by giving the program such large high resolution images it can't possibly use.Re-sizing in a bulk processing software and creating a file with these re-sized images in will speed up the rendering time enormously. By using an image editing program you can apply such things as sharpening at the new resolution which improves image quality a lot.

A better method is to store a lower res Jpeg (not lower quality) in camera then the camera will sharpen and process them for you. The only problem is you can't easily print the still images, but your camera will also have a Raw + Jpeg setting (or should have), the Jpeg will be at whatever res you set, you can set a low res Jpeg in camera and still have the Raw file for editing and printing purposes. You can set the Jpeg conversion in the camera by altering the Saturation, Sharpening etc. To get decent images in camera. Using the Raw + Jpeg will take more room on the card, but cards are cheap these days and for this purpose you don't need a fast Class 6 or Class 10 card.