My mac become so slow i can't use any app. All the time there is sound of hard drive but no swapping is reported by system monitor.

Question

Hi Folks,
recently my Mac after latest upgrade of Maverics 10.9.2 degraded performance dramatically to the point that when I switch from one app to another i should wait 30-40 seconds to get the response back from the System. The Hard drive is in use each time I click a mouse button. Sounds like an excessive hard drive usage usually caused by swapping. But System monitor shows Free memory ) Swapping and plenty of Idle CPU.
I tried to find the Process that might over uses the disk but all appear to be Ok. i couldn't spot any process that would over use the IO.
IO looks normal from System Monitor.
I checked the Apple Support whenever it is a defected hard disk issue but according to serial this Mac is not under disk replacement program.
Any tips on what should I do to find the root cause?
Mac specifications:
27-inch Mid 2010
MEMORY 4GB 1333 MHZ DDR3
Software  OS X 10.9.2 (13C64)
ATI Radeon HD 5750 1024 MB graphics
Intel 5 Series Chipset:
  Vendor:          Intel
  Product:          5 Series Chipset
  Link Speed:          3 Gigabit
  Negotiated Link Speed:          3 Gigabit
  Physical Interconnect:          SATA
  Description:          AHCI Version 1.30 Supported
ST31000528AS:
  Capacity:          1 TB (1,000,204,886,016 bytes)
  Model:          ST31000528AS                           
  Revision:          AP25   
  Serial Number:                      9VP87BKN
  Native Command Queuing:          Yes
  Queue Depth:          32
  Removable Media:          No
  Detachable Drive:          No
  BSD Name:          disk0
  Rotational Rate:          7200
  Medium Type:          Rotational
  Partition Map Type:          GPT (GUID Partition Table)
  S.M.A.R.T. status:          Verified
Thanks in advance
Emile

Answer 1

I have plenty of disk space 350 GB free.
I don't run excessive number of apps as you can see in top I have plenty of free Physical RAm plenty of idle CPU and IO is Ok too Swap is not in use means there is no lack of any resources
Even I f I quit all applications and use just safari the problem exists.
Processes: 174 total, 2 running, 6 stuck, 166 sleeping, 813 threads                                                11:35:05
Load Avg: 0.79, 0.78, 0.46  CPU usage: 0.47% user, 1.42% sys, 98.10% idle
SharedLibs: 134M resident, 0B data, 21M linkedit. MemRegions: 23450 total, 1500M resident, 121M private, 411M shared.
PhysMem: 3342M used (539M wired), 747M unused. VM: 418G vsize, 1310M framework vsize, 0(0) swapins, 0(0) swapouts.
Networks: packets: 25114/24M in, 16805/2740K out. Disks: 67293/2231M read, 15086/343M written.
I don't run any MAc keeper like apps nor antiviruses . I don't trust them. I f I need to clean something I will do it myself
Happens in switch between all apps even between the tabs in safari
The only symptom I have so far is noisy hard disk
each time i switch apps or windows I hear hard disk doing something.
Makes me think it might be hard disk problem but fsck doesn't show any issue
no bad secktors etc.
According to all diagnostics everything is Ok
That's kind of worries me not to be able to find the bottleneck having more than 20 years experience with UNIX