In my 10 gallon cichlid fry tank, I have no substrate, and I have one plant in there for them to rest on at night. (They are literally using the plant like a bed its pretty funny)
If you go and buy the smallest siphon you can find then take the end off of it so it looks like a regular hose, you can put the hose almost flat against the bottom of the glass and slowly suck the water and 'stuff' off the bottom. If you accidently suck one up, no worries, just keep an eye on the siphon at all times, and check your bucket before you pour it out.