How was the art made...in ID? What PDF profle are you exporting to?
I made the large logo in Illustrator, and I downloaded the small icons (128x128, and resized). I tried both interactive and print, and it looked the same. But even when I printed directly from inDesign, it still doesn't look good...
Did you place the AI file? Or export it as some image type?
The facebook/twitter circle logos. Are the low-res bitmaps or vector? If you need to, click on these logos and look at the links panel. Should tell you the placed and effective resolution if they are bitmaps.
For the PDF export, try the PDFX-4 export.
Seems to me that the export options for the pdf aren't good. Indeed, try PDFX-4. If the circle in ILL is ok, place the AI-file (no copy-paste) in ID. Did it look good on screen? If it's already "not good looking", then the problems come form the imported files. Does the text looks ok when printed?
The little icons: resolution is too low to get a good print. Try finding a better file (search for a vector image).
128x128 tells us nothing. Select one and open the info panel. What is the effective resolution?
FWIW, I'm sure if spent a little time you'd be able to find vector versions of those logos.