if the bypass tube cracked they likely neglected the coolant leak long enought that the engine was severely overheated. $25 is a good price because of the extreme heat it would take to actually damage the aluminum makes it unlikely the new part will be bad. intake manifolds are common on these engines because of gm's use of dex cool & poor gasket design. if the manifold is actually cracked then there are probably some other seriouse issues with the engine. however the bypass tube adapter may be replaced depending on your engine. knowing which engine you have could help. long story short, i wouldn't buy new parts on an engine that is likely damaged. put on a used part & use plenty of right stuff gasket maker.
I'm replacing this for a neighbor. He's a trucker, wife is home,. They have been putting JB weld around the bypass tube because the thermostat housing cracked. I don't know the how's or why's but it's cracked. I thought someone might know a dealer for this part, I have a junk yard with one for $25. Right now that's my best bet, I've seen one new one online for$300.
You should be able to purchase and intake manifold for your 2003 Chevrolet Malibu from any of the sources you listed in your question. I have a question back to you, Why do you need a new intake manifold? If your Malibu has a V6 engine manifold leaks are not uncommon but do not usually require replacement of the manifold itself. In most cases manifold gasket replacement will correct any leaks.