Could you add a link to the PH-probe ?
I read that a glass-PH-probe could be 800MOhm, is that right ?
Do you use a good shielded cable, which is fully shielded at both ends ?
Some noise of the mains voltage is probably passed on to the water via inductive/capacitive coupling in the pumps. It is almost impossible to get rid of that (only if batteries are used to power the pumps).
An opticial isolation could work. A DC/DC converter with an transformer removes the ground loop, but also passes on noise. An input circuit with a battery could also do, and with a optocoupler to pass the digital signal to the Arduino.
You could do a test. Use a battery for the Arduino and sensor board. Don't connect the usb or anything else to the Arduino, and store the PH-value in EEPROM. After that, read the EEPROM and check the values. If those values are good, your circuit is good and the problem is the noise and the ground loop.
I'm sorry, but I couldn't find a good solution for a PH-sensor. You might have to buy such an isolated circuit as the SX10507. Using your Atlas Scientific Ph Stamps circuit board and making your own isolated data transfer is not easy.
Added: Now that I have thought about it, the best way to isolate it, is at the serial connection. You could use two optocouplers for the RX and TX signals. The Atlas Scientific Ph Stamp could be powered with an galvanically isolated DC-DC converter.
There are ic's for RS232 isolation, but two normal optocouplers is better. Like these: http://yusisukmalia.wordpress.com/2009/06/11/rs232-make-optocoupler/
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An isolated DC-DC converter is cheap if they have unregulated output:
DC/DC 1W isolated converter 5V IN 5V OUT MORNSUN F0505M-1W | eBay
But you have to test it, the output could be too noisy.