A number of pianists report having issues with rhythm. To help solve the problem we need to be able to set a steady pulse and to internalise this as we play, pushing and pulling according to the natural ebb and flow that virtually all music requires. This is vastly different from playing metronomically, since no performance of anything is going to conform to an unbending metronomic beat, and while a certain amount of metronome practice can be beneficial if you know what you’re doing, too much of it ends up being detrimental.
When I was a student at the Royal College of Music, we used Paul Hindemith’s Elementary Training for Musicians as a text book for handling complex rhythms against a steady pulse. Some of the exercises are pretty gruelling, and would challenge anyone. In this exercise, you are required to play the notes with one hand, but a tone higher than written, while tapping the rhythm below the stave on your knee (and then play again in two other stipulated keys). Yes, really…
Hindemith requires what he calls “coordinated action” in the exercises. This might involve speaking the given rhythm while conducting with one hand, or perhaps tapping it with the left hand while conducting with the right, tapping it with the foot while conducting, and so on – a literal embodiment of rhythm.
Rhythmic Training by Robert Starer
There is no doubt that practising the rigorous exercises in Hindemith’s book will prove beneficial for the more advanced player, but let’s start somewhere simpler. I can highly recommend a little book by Robert Starer, entitled Rhythmic Training. It’s been around for years, and is excellent if you follow the directions.
The author states in the preface:
The ability to transform visual symbols of rhythmic notation into time-dividing sounds is an acquired skill. It involves the coordination of physical, psychological, and musical factors and cannot, therefore, be accomplished by the simple act of comprehension. This book represents an attempt to develop and train the ability to read and perform musical rhythms accurately… It is intended for the classroom, for the private studio and for self-training.
The book starts with the basics, how rhythm is organised and with explanations of the concepts of bar line and meter. Starer deals with time signatures (simple and compound), changing meters, rhythmic concepts such as hemiola and polyrhythms. The exercises get harder as the book progresses. As in the Hindemith, you can sing (or vocalise on a neutral syllable) and tap, sing and conduct, play and tap, etc. So, in the following exercise you might conduct with one hand (the “strong-weak-weak” hierarchy represented on the one stave in the stems-down notation) and speak the rhythm (ta-a for the minims, ta for the crotchets; either say “rest” on the rests, or simply say nothing). 
In the final chapter we no longer find notation for the pulse and its suggested subdivisions, the idea is that by now we will have internalised these.
Other Resources
Most of the following resources contain links to Amazon, where you can preview the text to see if it might work for you.
The Rhythm Bible by Dan Fox
Musikal Husky Rhythm Keeper by Steve and Samantha Steitz (only available via Amazon US and EU it seems, although a UK edition is imminent)
Basic Timing for the Pianist by Alan Small
Rhythm Menagerie by Wendy Stevens
Let me leave you with a wonderful example of embodied rhythm, Don Swanson with Nigerian master drummer Baba Ayo Adeyemi.