Yes, there is an alternative. You can send or receive query options as JSON or XML instead of using the deprecated builder.
To expand a bit, the QueryOptionsManager.writeOptions() method accepts any class that implements the QueryOptionsWriteHandle marker interface. Besides the QueryOptionsHandle class, implementing classes include the write handles for JSON or XML.
Similarly, the readOptions() method accepts the classes that implement the QueryOptionsReadHandle marker interface, which include the read handles for JSON or XML.