Is there any way to have Boto seek for the configuration files other than the default location, which is ~/.aws?
It's not clear from the question whether you are talking about boto or boto3.  Both allow you to use environment variables to tell it where to look for credentials and configuration files but the environment variables are different.
In boto3 you can use the environment variable AWS_SHARED_CREDENTIALS_FILE to tell boto3 where your credentials file is (by default, it is in ~/.aws/credentials.  You can use AWS_CONFIG_FILE to tell it where your config file is (by default, it is in ~/.aws/config.
In boto, you can use BOTO_CONFIG to tell boto where to find its config file (by default it is in /etc/boto.cfg or ~/.boto.
Boto3: Configuration file location