Currently you cannot easily configure the log levels for the Tooling API.
The tooling API is divided into consumer piece (the tooling api jar) and the provider piece (basically the target gradle you connect to). The log levels for consumer you should be able to configure in slf4j regular way, e.g. use configurable implementation of slf4j (for example, log4j), prepare the configuration and make sure the configuration is consumed (for log4j that would be log4.properties somewhere on the classpath).
However, for the provider you cannot easily change the log levels at the moment. I'm creating a jira ticket for it and I'm pretty sure we want to fix it soon.
The only workaround that comes to my mind is wrapping your System.out with something that can filter out the tooling api debug entries. I know it's not beautiful - we'll fix this problem definitely. Thanks for reporting!